From Genome Analysis Wiki
and exit when trying to run on an already mark-duplicated BAM
--excludeFlags <flag> : exclude reads with any of these flags set when determining or marking duplicates
by default (
0x304): exclude unmapped, secondary reads, and QC failures
--verbose : Turn on verbose mode
--noeof : Do not expect an EOF block on a bam file.
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
Skip records with any of the specified flags set, default
By default skips reads with any of the following flags set:
* secondary alignment
* fails QC checks
This parameter was added in version 1.0.10.